Lovely post! A nice addition to the topic, which clearly points out the issues that arise when splitting lines on more complex routes. I just ran into the exact situation you described while watching the traffic flow at a terminal station.
The workaround would be a number of parallel waiting tracks outside the station and hope for the best or the same amount of tracks on the stations as there is lines and hope that the game splits the lines evenly over the number of tracks.
Yeah, this is how I do it now, but you can forget about keeping things compact this way. I prefer the tracks being outside the station, so that I can still fit the station in the middle of a dense city. But when there’s no space restrictions (most industrial setups), I might just as well build an extra large station where every line gets its own lane.
This shows there is quite a big weakness in the path finding system of TF. Actually as some earlier pointed out OpenTTD has a path finding system that works great.
I prefer the traditional OpenTTD method as well, I still have to get the hang of Train Fever and it seems it’s still possible to make neat looking configurations, but I hoped Train Fever would be a step forwards in all aspects, not in just some.